Multiple destinations, no.  By definition there can be only one destination.

Multiple waypoints, yes.  The flight planner tries to create an optimal flight plan but waypoints can be deleted or added in the built in flight plan editor.

To add a waypoint drag the flight path line to it.

This may sound weird, but here goes:

1) Plot out your flight plan using a sectional (or go to skyvector.com), noting your waypoints.

2) Start the sim, go to the Flight Planner, create your flight plan using your 1st waypoint, save it and initialize the flight.

3) When you get within 5 mi. of your 1st waypoint, use the GPS program function to enter your next waypoint into the GPS (intersections, VOR's, airports). DO NOT HIT 'ENTER'.

4) when you get within 1 mi of your waypoint, scroll through the GPS menu back to the waypoint info you entered, then HIT 'ENTER'.

5) Follow the Director (green line) to the next waypoint!

Did that make any sense? When I fly VFR cross country flights, I use this method with the GPS. I also use the Sectionals from SkyVector on another laptop to plot my flight plan, going from waypoint to waypoint.

Northwest... you are a pilot, right? I'm not, and I'm wondering if this is the way pilots use the charts for VFR flight?

Hope this wasn't too confusing! 

Alan